Starting phenix.real_space_refine on Mon Sep 14 06:18:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qld_4579/09_2026/6qld_4579.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qld_4579/09_2026/6qld_4579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qld_4579/09_2026/6qld_4579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qld_4579/09_2026/6qld_4579.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qld_4579/09_2026/6qld_4579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qld_4579/09_2026/6qld_4579.map" } resolution = 4.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 76 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 248 5.49 5 S 86 5.16 5 C 17735 2.51 5 N 5188 2.21 5 O 5829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29086 Number of models: 1 Model: "" Number of chains: 22 Chain: "C" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 194 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Chain: "G" Number of atoms: 2524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2524 Classifications: {'DNA': 124} Link IDs: {'rna3p': 123} Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 948 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 12, 'GLN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 79 Chain: "I" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2701 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 335 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASN:plan1': 9, 'ARG:plan': 5, 'ASP:plan': 11, 'GLU:plan': 11, 'GLN:plan1': 2, 'TYR:plan': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 175 Chain: "J" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2560 Classifications: {'DNA': 124} Link IDs: {'rna3p': 123} Chain: "K" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 774 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "L" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1937 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 231} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2929 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 20, 'TRANS': 350} Chain breaks: 5 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 1, 'GLU:plan': 8, 'TRP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 71 Chain: "O" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1658 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "P" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1865 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 6, 'TRANS': 235} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 92 Chain: "Q" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1421 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain breaks: 3 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 15, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 156 Chain: "U" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1229 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 11, 'PHE:plan': 3, 'ASN:plan1': 3, 'GLU:plan': 6, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "Y" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1541 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 15, 'TYR:plan': 1, 'GLU:plan': 16, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 138 Chain: "Z" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 995 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'GLN:plan1': 5, 'HIS:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "a" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 706 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 625 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 719 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "e" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 801 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain breaks: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "f" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "g" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 813 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "h" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "i" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 788 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Time building chain proxies: 5.53, per 1000 atoms: 0.19 Number of scatterers: 29086 At special positions: 0 Unit cell: (183.12, 226.72, 135.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 86 16.00 P 248 15.00 O 5829 8.00 N 5188 7.00 C 17735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.1 seconds 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6076 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 15 sheets defined 64.2% alpha, 6.6% beta 120 base pairs and 204 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'H' and resid 5 through 38 Processing helix chain 'H' and resid 46 through 73 Processing helix chain 'H' and resid 83 through 93 Processing helix chain 'H' and resid 96 through 135 Processing helix chain 'I' and resid 334 through 338 removed outlier: 4.199A pdb=" N HIS I 338 " --> pdb=" O SER I 335 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 349 removed outlier: 3.553A pdb=" N SER I 349 " --> pdb=" O LEU I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 369 removed outlier: 3.505A pdb=" N GLU I 358 " --> pdb=" O SER I 354 " (cutoff:3.500A) Processing helix chain 'I' and resid 378 through 387 Processing helix chain 'I' and resid 389 through 399 Processing helix chain 'I' and resid 402 through 407 Processing helix chain 'I' and resid 409 through 421 Processing helix chain 'I' and resid 432 through 450 Processing helix chain 'I' and resid 457 through 473 removed outlier: 4.125A pdb=" N THR I 461 " --> pdb=" O THR I 457 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN I 471 " --> pdb=" O GLN I 467 " (cutoff:3.500A) Processing helix chain 'I' and resid 479 through 493 Processing helix chain 'I' and resid 506 through 524 Processing helix chain 'I' and resid 538 through 548 Processing helix chain 'I' and resid 550 through 569 Processing helix chain 'I' and resid 577 through 592 Processing helix chain 'I' and resid 607 through 619 removed outlier: 3.521A pdb=" N PHE I 611 " --> pdb=" O SER I 607 " (cutoff:3.500A) Processing helix chain 'I' and resid 639 through 651 Processing helix chain 'I' and resid 666 through 675 Processing helix chain 'I' and resid 695 through 707 removed outlier: 3.776A pdb=" N THR I 707 " --> pdb=" O HIS I 703 " (cutoff:3.500A) Processing helix chain 'I' and resid 712 through 721 Processing helix chain 'I' and resid 722 through 726 removed outlier: 3.508A pdb=" N SER I 726 " --> pdb=" O LYS I 723 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 40 Processing helix chain 'K' and resid 51 through 58 Processing helix chain 'K' and resid 70 through 127 Processing helix chain 'L' and resid 19 through 28 Processing helix chain 'L' and resid 94 through 106 Processing helix chain 'L' and resid 118 through 128 Processing helix chain 'L' and resid 153 through 157 Processing helix chain 'L' and resid 166 through 178 Processing helix chain 'L' and resid 182 through 187 removed outlier: 3.618A pdb=" N ASP L 186 " --> pdb=" O HIS L 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 196 Processing helix chain 'L' and resid 229 through 240 removed outlier: 3.609A pdb=" N LEU L 233 " --> pdb=" O ARG L 229 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 25 removed outlier: 3.827A pdb=" N VAL N 20 " --> pdb=" O ASP N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 43 removed outlier: 3.530A pdb=" N LEU N 32 " --> pdb=" O PRO N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 54 through 64 removed outlier: 3.868A pdb=" N LEU N 58 " --> pdb=" O LEU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 77 removed outlier: 3.924A pdb=" N ILE N 71 " --> pdb=" O ARG N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 100 Processing helix chain 'N' and resid 124 through 137 removed outlier: 3.624A pdb=" N PHE N 128 " --> pdb=" O GLN N 124 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE N 129 " --> pdb=" O PRO N 125 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU N 130 " --> pdb=" O ALA N 126 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN N 131 " --> pdb=" O LYS N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 218 through 232 Processing helix chain 'N' and resid 250 through 259 Processing helix chain 'N' and resid 261 through 265 removed outlier: 4.492A pdb=" N GLU N 265 " --> pdb=" O ARG N 262 " (cutoff:3.500A) Processing helix chain 'N' and resid 268 through 273 removed outlier: 4.397A pdb=" N CYS N 272 " --> pdb=" O PRO N 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 289 through 294 Processing helix chain 'N' and resid 318 through 334 Processing helix chain 'N' and resid 408 through 419 Processing helix chain 'N' and resid 423 through 427 removed outlier: 3.598A pdb=" N VAL N 427 " --> pdb=" O ILE N 424 " (cutoff:3.500A) Processing helix chain 'N' and resid 428 through 433 removed outlier: 3.661A pdb=" N GLY N 433 " --> pdb=" O GLY N 429 " (cutoff:3.500A) Processing helix chain 'O' and resid 154 through 172 Processing helix chain 'O' and resid 246 through 253 Processing helix chain 'O' and resid 254 through 257 removed outlier: 3.813A pdb=" N LEU O 257 " --> pdb=" O ASN O 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 254 through 257' Processing helix chain 'O' and resid 260 through 291 removed outlier: 3.583A pdb=" N ALA O 264 " --> pdb=" O SER O 260 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE O 267 " --> pdb=" O ASP O 263 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE O 285 " --> pdb=" O ARG O 281 " (cutoff:3.500A) Processing helix chain 'O' and resid 340 through 348 removed outlier: 3.591A pdb=" N LEU O 348 " --> pdb=" O TRP O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 352 through 363 removed outlier: 3.607A pdb=" N GLU O 356 " --> pdb=" O LEU O 352 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN O 360 " --> pdb=" O GLU O 356 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS O 361 " --> pdb=" O LEU O 357 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER O 362 " --> pdb=" O LYS O 358 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 110 Processing helix chain 'P' and resid 133 through 140 removed outlier: 3.880A pdb=" N THR P 140 " --> pdb=" O LYS P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 159 Processing helix chain 'P' and resid 224 through 232 removed outlier: 4.262A pdb=" N GLN P 230 " --> pdb=" O LEU P 226 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU P 231 " --> pdb=" O LYS P 227 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 266 Processing helix chain 'P' and resid 333 through 348 removed outlier: 4.017A pdb=" N LEU P 337 " --> pdb=" O ASN P 333 " (cutoff:3.500A) Processing helix chain 'P' and resid 352 through 363 Processing helix chain 'Q' and resid 162 through 184 Processing helix chain 'Q' and resid 197 through 219 removed outlier: 3.657A pdb=" N LEU Q 206 " --> pdb=" O LYS Q 202 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU Q 207 " --> pdb=" O LYS Q 203 " (cutoff:3.500A) Processing helix chain 'Q' and resid 234 through 293 Processing helix chain 'Q' and resid 322 through 333 Processing helix chain 'Q' and resid 349 through 357 Processing helix chain 'Q' and resid 358 through 382 removed outlier: 4.032A pdb=" N GLU Q 362 " --> pdb=" O PRO Q 358 " (cutoff:3.500A) Processing helix chain 'Q' and resid 382 through 391 removed outlier: 3.829A pdb=" N PHE Q 390 " --> pdb=" O ILE Q 386 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL Q 391 " --> pdb=" O LYS Q 387 " (cutoff:3.500A) Processing helix chain 'U' and resid 132 through 155 Proline residue: U 152 - end of helix Processing helix chain 'U' and resid 167 through 231 removed outlier: 3.594A pdb=" N LYS U 172 " --> pdb=" O LYS U 168 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU U 173 " --> pdb=" O LEU U 169 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP U 174 " --> pdb=" O LEU U 170 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU U 175 " --> pdb=" O TYR U 171 " (cutoff:3.500A) Processing helix chain 'U' and resid 233 through 265 removed outlier: 3.848A pdb=" N LEU U 264 " --> pdb=" O THR U 260 " (cutoff:3.500A) Processing helix chain 'U' and resid 288 through 299 Processing helix chain 'U' and resid 305 through 318 removed outlier: 3.845A pdb=" N GLU U 314 " --> pdb=" O ASN U 310 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 16 removed outlier: 3.700A pdb=" N SER Y 7 " --> pdb=" O ASP Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 22 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 57 through 83 removed outlier: 3.880A pdb=" N SER Y 76 " --> pdb=" O GLU Y 72 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 103 removed outlier: 3.871A pdb=" N ARG Y 98 " --> pdb=" O GLY Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 109 through 118 removed outlier: 3.567A pdb=" N LEU Y 118 " --> pdb=" O ILE Y 114 " (cutoff:3.500A) Processing helix chain 'Y' and resid 137 through 186 Processing helix chain 'Y' and resid 189 through 196 Processing helix chain 'Y' and resid 196 through 219 removed outlier: 3.695A pdb=" N PHE Y 219 " --> pdb=" O ALA Y 215 " (cutoff:3.500A) Processing helix chain 'Y' and resid 223 through 238 removed outlier: 4.343A pdb=" N LYS Y 238 " --> pdb=" O SER Y 234 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 14 removed outlier: 3.549A pdb=" N ASN Z 9 " --> pdb=" O GLN Z 5 " (cutoff:3.500A) Processing helix chain 'Z' and resid 19 through 23 removed outlier: 3.609A pdb=" N PHE Z 22 " --> pdb=" O LEU Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 43 Processing helix chain 'Z' and resid 43 through 82 removed outlier: 3.918A pdb=" N ALA Z 48 " --> pdb=" O GLU Z 44 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR Z 54 " --> pdb=" O ASP Z 50 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER Z 55 " --> pdb=" O ALA Z 51 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA Z 59 " --> pdb=" O SER Z 55 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG Z 60 " --> pdb=" O GLU Z 56 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG Z 71 " --> pdb=" O THR Z 67 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER Z 78 " --> pdb=" O ARG Z 74 " (cutoff:3.500A) Processing helix chain 'Z' and resid 88 through 124 removed outlier: 3.745A pdb=" N ASN Z 124 " --> pdb=" O ALA Z 120 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 152 removed outlier: 4.221A pdb=" N ALA Z 135 " --> pdb=" O ALA Z 131 " (cutoff:3.500A) Proline residue: Z 137 - end of helix Processing helix chain 'a' and resid 138 through 146 removed outlier: 4.316A pdb=" N ILE a 142 " --> pdb=" O ALA a 138 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN a 146 " --> pdb=" O ILE a 142 " (cutoff:3.500A) Processing helix chain 'a' and resid 155 through 170 Processing helix chain 'a' and resid 179 through 208 removed outlier: 4.343A pdb=" N LEU a 203 " --> pdb=" O GLU a 199 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU a 204 " --> pdb=" O HIS a 200 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU a 206 " --> pdb=" O ASN a 202 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA a 208 " --> pdb=" O LEU a 204 " (cutoff:3.500A) Processing helix chain 'a' and resid 216 through 221 Processing helix chain 'a' and resid 222 through 225 Processing helix chain 'b' and resid 31 through 43 Processing helix chain 'b' and resid 49 through 77 removed outlier: 4.485A pdb=" N GLU b 53 " --> pdb=" O GLY b 49 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU b 64 " --> pdb=" O LYS b 60 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N SER b 65 " --> pdb=" O SER b 61 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL b 66 " --> pdb=" O PHE b 62 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 95 Processing helix chain 'd' and resid 41 through 53 removed outlier: 3.509A pdb=" N GLN d 51 " --> pdb=" O LYS d 47 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR d 52 " --> pdb=" O VAL d 48 " (cutoff:3.500A) Processing helix chain 'd' and resid 59 through 88 removed outlier: 3.643A pdb=" N MET d 63 " --> pdb=" O SER d 59 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN d 88 " --> pdb=" O LEU d 84 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 106 removed outlier: 3.839A pdb=" N ILE d 98 " --> pdb=" O SER d 94 " (cutoff:3.500A) Processing helix chain 'd' and resid 107 through 128 Processing helix chain 'e' and resid 113 through 128 Processing helix chain 'e' and resid 139 through 146 removed outlier: 4.148A pdb=" N ARG e 143 " --> pdb=" O LEU e 139 " (cutoff:3.500A) Processing helix chain 'e' and resid 154 through 167 Processing helix chain 'e' and resid 179 through 208 removed outlier: 3.503A pdb=" N ILE e 183 " --> pdb=" O GLN e 179 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU e 203 " --> pdb=" O GLU e 199 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU e 204 " --> pdb=" O HIS e 200 " (cutoff:3.500A) Processing helix chain 'e' and resid 216 through 224 removed outlier: 3.917A pdb=" N LEU e 220 " --> pdb=" O LYS e 216 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA e 221 " --> pdb=" O ASP e 217 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ARG e 222 " --> pdb=" O MET e 218 " (cutoff:3.500A) Processing helix chain 'f' and resid 26 through 30 removed outlier: 4.336A pdb=" N ILE f 30 " --> pdb=" O ILE f 27 " (cutoff:3.500A) Processing helix chain 'f' and resid 31 through 42 Processing helix chain 'f' and resid 50 through 77 removed outlier: 4.299A pdb=" N GLU f 54 " --> pdb=" O LEU f 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP f 69 " --> pdb=" O SER f 65 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR f 74 " --> pdb=" O SER f 70 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 94 Processing helix chain 'g' and resid 28 through 40 removed outlier: 4.217A pdb=" N VAL g 32 " --> pdb=" O PRO g 28 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN g 40 " --> pdb=" O LEU g 36 " (cutoff:3.500A) Processing helix chain 'g' and resid 47 through 75 removed outlier: 4.381A pdb=" N VAL g 51 " --> pdb=" O SER g 47 " (cutoff:3.500A) Processing helix chain 'g' and resid 81 through 90 Processing helix chain 'g' and resid 92 through 99 Processing helix chain 'h' and resid 41 through 53 Processing helix chain 'h' and resid 59 through 88 Processing helix chain 'h' and resid 94 through 106 removed outlier: 4.026A pdb=" N ILE h 98 " --> pdb=" O SER h 94 " (cutoff:3.500A) Processing helix chain 'h' and resid 107 through 126 Processing helix chain 'i' and resid 28 through 38 Processing helix chain 'i' and resid 48 through 74 removed outlier: 3.818A pdb=" N TYR i 52 " --> pdb=" O GLY i 48 " (cutoff:3.500A) Processing helix chain 'i' and resid 81 through 91 removed outlier: 3.523A pdb=" N ASN i 91 " --> pdb=" O LEU i 87 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 100 Processing sheet with id=AA1, first strand: chain 'L' and resid 73 through 76 removed outlier: 3.533A pdb=" N PHE L 86 " --> pdb=" O LEU L 76 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N MET L 85 " --> pdb=" O ILE L 10 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR L 3 " --> pdb=" O THR L 223 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR L 223 " --> pdb=" O TYR L 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 33 through 36 removed outlier: 4.221A pdb=" N ASP L 34 " --> pdb=" O GLU L 57 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU L 57 " --> pdb=" O ASP L 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 130 through 132 Processing sheet with id=AA4, first strand: chain 'L' and resid 162 through 164 Processing sheet with id=AA5, first strand: chain 'N' and resid 106 through 110 removed outlier: 7.208A pdb=" N ILE N 210 " --> pdb=" O PRO N 205 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N TYR N 201 " --> pdb=" O SER N 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 106 through 110 removed outlier: 7.208A pdb=" N ILE N 210 " --> pdb=" O PRO N 205 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N TYR N 201 " --> pdb=" O SER N 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 112 through 113 removed outlier: 3.505A pdb=" N ARG N 113 " --> pdb=" O LYS N 117 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS N 117 " --> pdb=" O ARG N 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'O' and resid 175 through 180 removed outlier: 3.928A pdb=" N LEU O 180 " --> pdb=" O MET O 201 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N MET O 201 " --> pdb=" O LEU O 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 305 through 309 removed outlier: 6.028A pdb=" N LYS O 320 " --> pdb=" O ILE O 324 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ILE O 324 " --> pdb=" O LYS O 320 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY O 350 " --> pdb=" O ILE O 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 165 through 175 removed outlier: 5.669A pdb=" N VAL P 167 " --> pdb=" O LYS P 188 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LYS P 188 " --> pdb=" O VAL P 167 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL P 169 " --> pdb=" O ASN P 186 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN P 186 " --> pdb=" O VAL P 169 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER P 171 " --> pdb=" O VAL P 184 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE P 180 " --> pdb=" O VAL P 175 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU P 181 " --> pdb=" O TYR P 205 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE P 197 " --> pdb=" O PHE P 189 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU P 198 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ILE P 220 " --> pdb=" O GLU P 198 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN P 200 " --> pdb=" O LEU P 218 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS P 214 " --> pdb=" O PHE P 204 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 270 through 273 removed outlier: 3.769A pdb=" N ARG P 270 " --> pdb=" O GLU P 283 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU P 283 " --> pdb=" O ARG P 270 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET P 318 " --> pdb=" O THR P 303 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER P 319 " --> pdb=" O MET Q 335 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'b' and resid 97 through 99 removed outlier: 6.314A pdb=" N THR b 97 " --> pdb=" O THR g 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'd' and resid 57 through 58 removed outlier: 7.501A pdb=" N GLY d 57 " --> pdb=" O ILE i 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'd' and resid 92 through 93 Processing sheet with id=AB6, first strand: chain 'e' and resid 177 through 178 removed outlier: 7.453A pdb=" N ARG e 177 " --> pdb=" O VAL f 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 1560 hydrogen bonds defined for protein. 4617 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 310 hydrogen bonds 620 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 204 stacking parallelities Total time for adding SS restraints: 6.05 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7413 1.34 - 1.46: 6957 1.46 - 1.58: 15030 1.58 - 1.70: 492 1.70 - 1.82: 145 Bond restraints: 30037 Sorted by residual: bond pdb=" O3' DG G 4 " pdb=" P DA G 5 " ideal model delta sigma weight residual 1.607 1.458 0.149 1.20e-02 6.94e+03 1.54e+02 bond pdb=" O3' DT J -5 " pdb=" P DC J -4 " ideal model delta sigma weight residual 1.607 1.534 0.073 1.20e-02 6.94e+03 3.67e+01 bond pdb=" C3' DC G 78 " pdb=" O3' DC G 78 " ideal model delta sigma weight residual 1.435 1.483 -0.048 1.30e-02 5.92e+03 1.36e+01 bond pdb=" C3' DT J -91 " pdb=" O3' DT J -91 " ideal model delta sigma weight residual 1.435 1.483 -0.048 1.30e-02 5.92e+03 1.34e+01 bond pdb=" C3' DC G 45 " pdb=" C2' DC G 45 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.30e+01 ... (remaining 30032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.58: 41634 6.58 - 13.16: 53 13.16 - 19.73: 4 19.73 - 26.31: 0 26.31 - 32.89: 1 Bond angle restraints: 41692 Sorted by residual: angle pdb=" O3' DG G 4 " pdb=" P DA G 5 " pdb=" OP1 DA G 5 " ideal model delta sigma weight residual 108.00 75.11 32.89 3.00e+00 1.11e-01 1.20e+02 angle pdb=" C3' DT J -5 " pdb=" O3' DT J -5 " pdb=" P DC J -4 " ideal model delta sigma weight residual 119.70 106.66 13.04 1.20e+00 6.94e-01 1.18e+02 angle pdb=" O3' DG G 4 " pdb=" P DA G 5 " pdb=" O5' DA G 5 " ideal model delta sigma weight residual 104.00 121.03 -17.03 1.90e+00 2.77e-01 8.03e+01 angle pdb=" O3' DT J -5 " pdb=" P DC J -4 " pdb=" O5' DC J -4 " ideal model delta sigma weight residual 104.00 90.89 13.11 1.90e+00 2.77e-01 4.76e+01 angle pdb=" O4' DC G 107 " pdb=" C4' DC G 107 " pdb=" C3' DC G 107 " ideal model delta sigma weight residual 106.00 102.44 3.56 6.00e-01 2.78e+00 3.52e+01 ... (remaining 41687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.88: 16019 34.88 - 69.76: 1478 69.76 - 104.64: 38 104.64 - 139.52: 2 139.52 - 174.40: 1 Dihedral angle restraints: 17538 sinusoidal: 8258 harmonic: 9280 Sorted by residual: dihedral pdb=" CA MET P 274 " pdb=" C MET P 274 " pdb=" N ASN P 275 " pdb=" CA ASN P 275 " ideal model delta harmonic sigma weight residual -180.00 -151.09 -28.91 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA TYR N 77 " pdb=" C TYR N 77 " pdb=" N VAL N 78 " pdb=" CA VAL N 78 " ideal model delta harmonic sigma weight residual 180.00 153.70 26.30 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA SER N 266 " pdb=" C SER N 266 " pdb=" N MET N 267 " pdb=" CA MET N 267 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 17535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4064 0.061 - 0.122: 774 0.122 - 0.183: 103 0.183 - 0.244: 6 0.244 - 0.305: 2 Chirality restraints: 4949 Sorted by residual: chirality pdb=" CA PRO L 41 " pdb=" N PRO L 41 " pdb=" C PRO L 41 " pdb=" CB PRO L 41 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA ASP I 334 " pdb=" N ASP I 334 " pdb=" C ASP I 334 " pdb=" CB ASP I 334 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB ILE a 224 " pdb=" CA ILE a 224 " pdb=" CG1 ILE a 224 " pdb=" CG2 ILE a 224 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 4946 not shown) Planarity restraints: 4371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL L 40 " 0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C VAL L 40 " -0.058 2.00e-02 2.50e+03 pdb=" O VAL L 40 " 0.021 2.00e-02 2.50e+03 pdb=" N PRO L 41 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 297 " -0.016 2.00e-02 2.50e+03 3.13e-02 9.83e+00 pdb=" C TYR C 297 " 0.054 2.00e-02 2.50e+03 pdb=" O TYR C 297 " -0.020 2.00e-02 2.50e+03 pdb=" N TRP C 298 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG L 39 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.58e+00 pdb=" C ARG L 39 " 0.054 2.00e-02 2.50e+03 pdb=" O ARG L 39 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL L 40 " -0.018 2.00e-02 2.50e+03 ... (remaining 4368 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 7901 2.81 - 3.33: 25779 3.33 - 3.86: 51607 3.86 - 4.38: 54837 4.38 - 4.90: 89113 Nonbonded interactions: 229237 Sorted by model distance: nonbonded pdb=" OP1 DG G 102 " pdb=" N LYS f 80 " model vdw 2.289 3.120 nonbonded pdb=" O LEU I 701 " pdb=" OG SER I 705 " model vdw 2.294 3.040 nonbonded pdb=" OP2 DT G 31 " pdb=" NH2 ARG i 19 " model vdw 2.302 3.120 nonbonded pdb=" OG SER d 59 " pdb=" OG SER d 62 " model vdw 2.314 3.040 nonbonded pdb=" O SER O 214 " pdb=" OG SER O 214 " model vdw 2.315 3.040 ... (remaining 229232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'b' selection = (chain 'f' and (resid 25 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )) or resid 56 through 103)) } ncs_group { reference = chain 'd' selection = (chain 'h' and (resid 37 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 129)) } ncs_group { reference = (chain 'g' and resid 17 through 118) selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.650 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.149 30037 Z= 0.375 Angle : 0.904 32.888 41692 Z= 0.615 Chirality : 0.048 0.305 4949 Planarity : 0.005 0.062 4371 Dihedral : 21.698 174.403 11462 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.08 % Favored : 94.76 % Rotamer: Outliers : 0.25 % Allowed : 8.17 % Favored : 91.58 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.12), residues: 3051 helix: -1.89 (0.09), residues: 1896 sheet: -2.43 (0.32), residues: 234 loop : -2.90 (0.17), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 174 TYR 0.017 0.002 TYR O 170 PHE 0.021 0.002 PHE I 719 TRP 0.027 0.002 TRP I 472 HIS 0.006 0.001 HIS O 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.38 (30037) covalent geometry : angle 0.90402 / 0.61 (41692) hydrogen bonds : bond 0.13508 / 14.80 ( 1857) hydrogen bonds : angle 6.00366 / 7.83 ( 5237) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 664 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 55 ILE cc_start: 0.9354 (mt) cc_final: 0.9138 (mt) REVERT: H 56 ARG cc_start: 0.8418 (ttp80) cc_final: 0.7991 (ttt180) REVERT: H 65 LYS cc_start: 0.8631 (mtmm) cc_final: 0.8318 (tmtt) REVERT: I 346 ILE cc_start: 0.7852 (pt) cc_final: 0.7541 (tp) REVERT: I 364 LEU cc_start: 0.9377 (tp) cc_final: 0.8956 (mm) REVERT: I 512 PHE cc_start: 0.8359 (t80) cc_final: 0.8036 (t80) REVERT: I 516 LEU cc_start: 0.8944 (mt) cc_final: 0.8663 (tp) REVERT: I 612 LYS cc_start: 0.8500 (mttt) cc_final: 0.7987 (tptp) REVERT: K 22 LYS cc_start: 0.8455 (mttt) cc_final: 0.8073 (mmtt) REVERT: K 108 ASN cc_start: 0.7964 (m-40) cc_final: 0.7385 (p0) REVERT: L 121 MET cc_start: 0.8726 (mtp) cc_final: 0.8113 (mtp) REVERT: L 154 GLN cc_start: 0.8028 (mt0) cc_final: 0.7713 (tt0) REVERT: L 185 ASN cc_start: 0.7980 (t0) cc_final: 0.7471 (t0) REVERT: L 217 MET cc_start: 0.8167 (mtt) cc_final: 0.7847 (mtp) REVERT: N 25 MET cc_start: 0.8042 (mmm) cc_final: 0.7742 (tpt) REVERT: N 211 ILE cc_start: 0.8676 (mt) cc_final: 0.8457 (pt) REVERT: N 225 LEU cc_start: 0.9433 (tp) cc_final: 0.9111 (tp) REVERT: N 252 HIS cc_start: 0.7840 (m-70) cc_final: 0.7629 (m-70) REVERT: N 397 ILE cc_start: 0.9416 (mm) cc_final: 0.9040 (mt) REVERT: N 415 GLU cc_start: 0.8783 (tt0) cc_final: 0.8550 (tt0) REVERT: N 443 MET cc_start: 0.7941 (tpt) cc_final: 0.7639 (tpp) REVERT: O 164 ILE cc_start: 0.9521 (mt) cc_final: 0.9243 (mm) REVERT: O 237 LYS cc_start: 0.9450 (mmtt) cc_final: 0.9093 (mmmt) REVERT: O 262 ASP cc_start: 0.7915 (p0) cc_final: 0.6873 (t0) REVERT: O 277 GLU cc_start: 0.8471 (tt0) cc_final: 0.7648 (tm-30) REVERT: O 283 GLN cc_start: 0.9035 (tt0) cc_final: 0.8755 (tm-30) REVERT: O 305 MET cc_start: 0.7768 (ttm) cc_final: 0.7502 (tpp) REVERT: P 143 ASP cc_start: 0.7568 (p0) cc_final: 0.7273 (p0) REVERT: P 348 TYR cc_start: 0.7671 (m-10) cc_final: 0.7444 (m-10) REVERT: Q 251 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7968 (mm-30) REVERT: Q 331 GLU cc_start: 0.8975 (tt0) cc_final: 0.8704 (tt0) REVERT: Q 337 ASN cc_start: 0.8845 (t0) cc_final: 0.8541 (t0) REVERT: U 178 PHE cc_start: 0.7636 (m-80) cc_final: 0.7313 (m-10) REVERT: U 308 LYS cc_start: 0.8950 (mttt) cc_final: 0.8387 (tttt) REVERT: Y 59 GLN cc_start: 0.7636 (pt0) cc_final: 0.7260 (pt0) REVERT: Y 81 ILE cc_start: 0.7953 (tp) cc_final: 0.7741 (tp) REVERT: Y 155 GLN cc_start: 0.8410 (mt0) cc_final: 0.8001 (mt0) REVERT: a 160 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7091 (ptp-170) REVERT: a 179 GLN cc_start: 0.7803 (mt0) cc_final: 0.7364 (mp10) REVERT: a 183 ILE cc_start: 0.7404 (mm) cc_final: 0.6945 (tp) REVERT: a 193 TYR cc_start: 0.7986 (t80) cc_final: 0.7750 (t80) REVERT: a 195 VAL cc_start: 0.8452 (p) cc_final: 0.8231 (p) REVERT: b 54 GLU cc_start: 0.8594 (tp30) cc_final: 0.8357 (mt-10) REVERT: d 53 HIS cc_start: 0.7175 (m-70) cc_final: 0.6182 (m-70) REVERT: d 63 MET cc_start: 0.7997 (tpp) cc_final: 0.7593 (tpp) REVERT: d 120 ARG cc_start: 0.7685 (mtt180) cc_final: 0.7002 (ptt90) REVERT: e 163 LYS cc_start: 0.8178 (tttt) cc_final: 0.7399 (mptt) REVERT: e 164 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7286 (tm-30) REVERT: e 187 GLN cc_start: 0.8893 (tt0) cc_final: 0.8390 (tm-30) REVERT: e 223 ARG cc_start: 0.7880 (tmt-80) cc_final: 0.7496 (tpm170) REVERT: f 50 LEU cc_start: 0.8641 (tp) cc_final: 0.8118 (mp) REVERT: f 89 TYR cc_start: 0.8992 (m-10) cc_final: 0.8530 (m-80) REVERT: g 90 ARG cc_start: 0.8010 (mmt-90) cc_final: 0.7661 (ptt-90) REVERT: h 75 GLU cc_start: 0.8806 (tp30) cc_final: 0.8012 (tp30) REVERT: h 103 ARG cc_start: 0.7939 (tpt90) cc_final: 0.7133 (ttm-80) REVERT: i 44 ARG cc_start: 0.7396 (mtt-85) cc_final: 0.6926 (mtt-85) REVERT: i 58 GLU cc_start: 0.8538 (tt0) cc_final: 0.7840 (tm-30) REVERT: i 104 ILE cc_start: 0.8943 (mm) cc_final: 0.8497 (mt) REVERT: i 114 HIS cc_start: 0.6647 (t-90) cc_final: 0.6307 (t-90) outliers start: 6 outliers final: 2 residues processed: 669 average time/residue: 0.2154 time to fit residues: 217.3217 Evaluate side-chains 418 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 416 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.5980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 58 GLN H 113 GLN I 348 ASN I 376 GLN I 487 HIS I 582 ASN I 590 ASN I 613 GLN K 21 ASN K 111 ASN L 78 ASN L 131 HIS N 133 GLN O 283 GLN P 135 GLN P 223 ASN ** P 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 255 ASN U 217 ASN U 237 HIS U 310 ASN Y 158 GLN Y 198 ASN ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 202 ASN b 26 ASN g 75 ASN g 86 GLN g 91 ASN h 67 ASN i 116 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.109865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.087368 restraints weight = 109416.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.088663 restraints weight = 190500.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.089595 restraints weight = 95458.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.089647 restraints weight = 75624.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.090093 restraints weight = 66483.165| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30037 Z= 0.195 Angle : 0.677 13.343 41692 Z= 0.371 Chirality : 0.043 0.303 4949 Planarity : 0.006 0.161 4371 Dihedral : 24.065 170.309 6049 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.98 % Favored : 94.95 % Rotamer: Outliers : 0.08 % Allowed : 6.65 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.14), residues: 3051 helix: -0.03 (0.11), residues: 1926 sheet: -1.85 (0.33), residues: 235 loop : -2.53 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 210 TYR 0.021 0.002 TYR f 73 PHE 0.038 0.002 PHE I 512 TRP 0.013 0.001 TRP I 472 HIS 0.007 0.001 HIS i 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.20 (30037) covalent geometry : angle 0.67708 / 0.37 (41692) hydrogen bonds : bond 0.04701 / 4.94 ( 1857) hydrogen bonds : angle 4.34296 / 5.55 ( 5237) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 517 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 364 LEU cc_start: 0.9410 (tp) cc_final: 0.9086 (mm) REVERT: I 516 LEU cc_start: 0.8842 (mt) cc_final: 0.8428 (tp) REVERT: I 546 PHE cc_start: 0.8068 (m-80) cc_final: 0.7859 (m-80) REVERT: I 612 LYS cc_start: 0.8566 (mttt) cc_final: 0.8042 (tptp) REVERT: K 22 LYS cc_start: 0.8346 (mttt) cc_final: 0.7821 (mmtp) REVERT: K 108 ASN cc_start: 0.7807 (m-40) cc_final: 0.7416 (p0) REVERT: L 85 MET cc_start: 0.7553 (ttm) cc_final: 0.7338 (ttm) REVERT: L 121 MET cc_start: 0.8744 (mtp) cc_final: 0.8313 (mtp) REVERT: L 185 ASN cc_start: 0.7848 (t0) cc_final: 0.7442 (t0) REVERT: L 217 MET cc_start: 0.8357 (mtt) cc_final: 0.7954 (mtp) REVERT: N 25 MET cc_start: 0.8068 (mmm) cc_final: 0.7611 (tpp) REVERT: N 326 LEU cc_start: 0.9085 (mp) cc_final: 0.8799 (tp) REVERT: N 397 ILE cc_start: 0.9413 (mm) cc_final: 0.9109 (mt) REVERT: O 237 LYS cc_start: 0.9432 (mmtt) cc_final: 0.9078 (mmmm) REVERT: O 262 ASP cc_start: 0.7958 (p0) cc_final: 0.6842 (t0) REVERT: O 277 GLU cc_start: 0.8426 (tt0) cc_final: 0.7946 (tm-30) REVERT: O 321 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7829 (tm-30) REVERT: P 304 MET cc_start: 0.8683 (tpp) cc_final: 0.8469 (mmt) REVERT: Q 374 MET cc_start: 0.7681 (mtp) cc_final: 0.7405 (mtp) REVERT: U 178 PHE cc_start: 0.7556 (m-80) cc_final: 0.7302 (m-10) REVERT: U 308 LYS cc_start: 0.8881 (mttt) cc_final: 0.8397 (tptt) REVERT: Y 81 ILE cc_start: 0.8106 (tp) cc_final: 0.7889 (tp) REVERT: Y 155 GLN cc_start: 0.8119 (mt0) cc_final: 0.7895 (mt0) REVERT: a 160 ARG cc_start: 0.7866 (mtt180) cc_final: 0.7264 (mtp180) REVERT: a 179 GLN cc_start: 0.7786 (mt0) cc_final: 0.7376 (mp10) REVERT: d 53 HIS cc_start: 0.7227 (m-70) cc_final: 0.6136 (m-70) REVERT: d 63 MET cc_start: 0.7721 (tpp) cc_final: 0.7349 (tpp) REVERT: d 120 ARG cc_start: 0.7604 (mtt180) cc_final: 0.7001 (ptt90) REVERT: e 163 LYS cc_start: 0.8148 (tttt) cc_final: 0.7465 (mptt) REVERT: e 222 ARG cc_start: 0.7859 (mtp85) cc_final: 0.7447 (mtp85) REVERT: e 223 ARG cc_start: 0.7487 (tmt-80) cc_final: 0.7278 (tpm170) REVERT: f 50 LEU cc_start: 0.8341 (tp) cc_final: 0.7888 (mp) REVERT: g 34 ARG cc_start: 0.7200 (ttp-110) cc_final: 0.6576 (ptm-80) REVERT: g 90 ARG cc_start: 0.7846 (mmt-90) cc_final: 0.7589 (ttp-170) REVERT: h 75 GLU cc_start: 0.8748 (tp30) cc_final: 0.8137 (tp30) REVERT: h 87 TYR cc_start: 0.8619 (m-10) cc_final: 0.8332 (m-80) REVERT: i 58 GLU cc_start: 0.8138 (tt0) cc_final: 0.7663 (tm-30) REVERT: i 80 ILE cc_start: 0.8287 (mm) cc_final: 0.8048 (mm) REVERT: i 89 ILE cc_start: 0.7908 (tt) cc_final: 0.7679 (tt) REVERT: i 104 ILE cc_start: 0.8956 (mm) cc_final: 0.8625 (mt) outliers start: 2 outliers final: 1 residues processed: 519 average time/residue: 0.1992 time to fit residues: 160.6564 Evaluate side-chains 384 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 383 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 319 optimal weight: 9.9990 chunk 251 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 chunk 270 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 6 optimal weight: 50.0000 chunk 243 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 266 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 363 GLN I 467 GLN I 487 HIS K 111 ASN L 96 ASN N 73 ASN ** P 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 255 ASN ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 53 HIS ** d 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 174 GLN ** e 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 ASN i 75 ASN i 116 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.110456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.088103 restraints weight = 109026.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.089660 restraints weight = 183859.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.090475 restraints weight = 89848.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.090478 restraints weight = 72919.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.091009 restraints weight = 64924.474| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 30037 Z= 0.143 Angle : 0.615 10.542 41692 Z= 0.340 Chirality : 0.042 0.282 4949 Planarity : 0.005 0.135 4371 Dihedral : 24.034 170.946 6049 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.79 % Favored : 95.15 % Rotamer: Outliers : 0.04 % Allowed : 4.06 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.15), residues: 3051 helix: 0.79 (0.12), residues: 1925 sheet: -1.52 (0.34), residues: 234 loop : -2.32 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 119 TYR 0.023 0.002 TYR f 73 PHE 0.026 0.001 PHE Q 325 TRP 0.016 0.001 TRP P 326 HIS 0.005 0.001 HIS i 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (30037) covalent geometry : angle 0.61467 / 0.34 (41692) hydrogen bonds : bond 0.04130 / 4.35 ( 1857) hydrogen bonds : angle 4.01929 / 5.16 ( 5237) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 507 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 ARG cc_start: 0.7445 (tpt170) cc_final: 0.7175 (tpt90) REVERT: H 56 ARG cc_start: 0.8316 (ttp80) cc_final: 0.8014 (ttt90) REVERT: H 112 LYS cc_start: 0.8454 (mptt) cc_final: 0.8228 (mmtt) REVERT: I 364 LEU cc_start: 0.9274 (tp) cc_final: 0.9026 (tp) REVERT: I 612 LYS cc_start: 0.8580 (mttt) cc_final: 0.8025 (tptp) REVERT: I 712 ARG cc_start: 0.8023 (mtp-110) cc_final: 0.7776 (mtp180) REVERT: K 22 LYS cc_start: 0.8251 (mttt) cc_final: 0.7998 (mmtm) REVERT: K 108 ASN cc_start: 0.7755 (m-40) cc_final: 0.7401 (p0) REVERT: L 121 MET cc_start: 0.8731 (mtp) cc_final: 0.8254 (mtp) REVERT: L 217 MET cc_start: 0.8256 (mtt) cc_final: 0.8024 (mtp) REVERT: N 25 MET cc_start: 0.8083 (mmm) cc_final: 0.7795 (tpt) REVERT: N 265 GLU cc_start: 0.8039 (mp0) cc_final: 0.7696 (mp0) REVERT: N 397 ILE cc_start: 0.9412 (mm) cc_final: 0.9135 (mt) REVERT: N 425 ASP cc_start: 0.7984 (m-30) cc_final: 0.7737 (m-30) REVERT: O 237 LYS cc_start: 0.9382 (mmtt) cc_final: 0.9057 (mmmm) REVERT: O 262 ASP cc_start: 0.7946 (p0) cc_final: 0.7044 (t0) REVERT: O 277 GLU cc_start: 0.8296 (tt0) cc_final: 0.7938 (tm-30) REVERT: O 321 GLN cc_start: 0.8171 (tm-30) cc_final: 0.7904 (tm-30) REVERT: Q 239 SER cc_start: 0.9125 (m) cc_final: 0.8639 (t) REVERT: Q 374 MET cc_start: 0.7916 (mtp) cc_final: 0.7561 (mtp) REVERT: U 178 PHE cc_start: 0.7467 (m-80) cc_final: 0.7237 (m-10) REVERT: U 308 LYS cc_start: 0.8885 (mttt) cc_final: 0.8377 (tptt) REVERT: U 312 ILE cc_start: 0.8526 (mt) cc_final: 0.8195 (tp) REVERT: Y 102 GLU cc_start: 0.8256 (pp20) cc_final: 0.7504 (pp20) REVERT: Y 155 GLN cc_start: 0.8146 (mt0) cc_final: 0.7872 (mt0) REVERT: a 179 GLN cc_start: 0.7732 (mt0) cc_final: 0.7312 (mp10) REVERT: a 183 ILE cc_start: 0.7460 (tp) cc_final: 0.6899 (mm) REVERT: d 120 ARG cc_start: 0.7692 (mtt180) cc_final: 0.7052 (ptt90) REVERT: e 163 LYS cc_start: 0.7967 (tttt) cc_final: 0.7706 (ttmt) REVERT: g 34 ARG cc_start: 0.7564 (ttp-110) cc_final: 0.7039 (ptm-80) REVERT: g 90 ARG cc_start: 0.7695 (mmt-90) cc_final: 0.7377 (ttp80) REVERT: h 75 GLU cc_start: 0.8749 (tp30) cc_final: 0.8165 (tp30) REVERT: h 87 TYR cc_start: 0.8661 (m-10) cc_final: 0.8336 (m-80) REVERT: i 44 ARG cc_start: 0.7281 (mtt-85) cc_final: 0.6901 (mtp85) REVERT: i 58 GLU cc_start: 0.8043 (tt0) cc_final: 0.7599 (tm-30) REVERT: i 103 THR cc_start: 0.7904 (p) cc_final: 0.7698 (p) REVERT: i 104 ILE cc_start: 0.8936 (mm) cc_final: 0.8702 (mt) outliers start: 1 outliers final: 1 residues processed: 508 average time/residue: 0.1986 time to fit residues: 157.7752 Evaluate side-chains 386 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 385 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 101 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 210 optimal weight: 20.0000 chunk 228 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 257 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 57 HIS I 467 GLN I 487 HIS K 111 ASN ** P 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 255 ASN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 47 GLN ** Z 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 187 GLN ** b 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 207 HIS h 67 ASN i 116 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.109507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.087207 restraints weight = 108481.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.088091 restraints weight = 197959.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.089549 restraints weight = 105925.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.089554 restraints weight = 71386.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.089860 restraints weight = 63991.800| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30037 Z= 0.166 Angle : 0.627 9.601 41692 Z= 0.343 Chirality : 0.042 0.275 4949 Planarity : 0.005 0.137 4371 Dihedral : 24.029 170.945 6049 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.15 % Favored : 94.79 % Rotamer: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.16), residues: 3051 helix: 1.20 (0.12), residues: 1931 sheet: -1.40 (0.35), residues: 238 loop : -2.21 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG g 38 TYR 0.032 0.002 TYR d 87 PHE 0.037 0.002 PHE I 546 TRP 0.011 0.001 TRP C 298 HIS 0.006 0.001 HIS O 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (30037) covalent geometry : angle 0.62727 / 0.34 (41692) hydrogen bonds : bond 0.04114 / 4.28 ( 1857) hydrogen bonds : angle 3.89025 / 4.97 ( 5237) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 488 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 ARG cc_start: 0.7465 (tpt170) cc_final: 0.7222 (tpt90) REVERT: H 56 ARG cc_start: 0.8175 (ttp80) cc_final: 0.7893 (ttm110) REVERT: I 612 LYS cc_start: 0.8567 (mttt) cc_final: 0.8008 (tptp) REVERT: K 108 ASN cc_start: 0.7913 (m-40) cc_final: 0.7463 (p0) REVERT: L 121 MET cc_start: 0.8649 (mtp) cc_final: 0.8246 (mtp) REVERT: L 217 MET cc_start: 0.8317 (mtt) cc_final: 0.8023 (mtp) REVERT: N 25 MET cc_start: 0.8149 (mmm) cc_final: 0.7900 (tpt) REVERT: N 122 LYS cc_start: 0.8779 (mtmm) cc_final: 0.8456 (ptpp) REVERT: N 265 GLU cc_start: 0.8016 (mp0) cc_final: 0.7687 (mp0) REVERT: N 397 ILE cc_start: 0.9418 (mm) cc_final: 0.9133 (mt) REVERT: N 425 ASP cc_start: 0.8000 (m-30) cc_final: 0.7794 (m-30) REVERT: O 201 MET cc_start: 0.8405 (mtp) cc_final: 0.8146 (ttp) REVERT: O 237 LYS cc_start: 0.9370 (mmtt) cc_final: 0.9061 (mmmm) REVERT: O 262 ASP cc_start: 0.8006 (p0) cc_final: 0.7210 (t0) REVERT: O 277 GLU cc_start: 0.8441 (tt0) cc_final: 0.7864 (tm-30) REVERT: O 321 GLN cc_start: 0.8084 (tm-30) cc_final: 0.7710 (tm-30) REVERT: P 143 ASP cc_start: 0.7676 (p0) cc_final: 0.7262 (p0) REVERT: Q 239 SER cc_start: 0.9124 (m) cc_final: 0.8626 (t) REVERT: Q 374 MET cc_start: 0.7904 (mtp) cc_final: 0.7631 (mtp) REVERT: U 178 PHE cc_start: 0.7516 (m-80) cc_final: 0.7288 (m-10) REVERT: U 308 LYS cc_start: 0.8853 (mttt) cc_final: 0.8369 (tttt) REVERT: U 312 ILE cc_start: 0.8455 (mt) cc_final: 0.8109 (tp) REVERT: Y 155 GLN cc_start: 0.8262 (mt0) cc_final: 0.7933 (mt0) REVERT: a 179 GLN cc_start: 0.7847 (mt0) cc_final: 0.7313 (mp10) REVERT: d 120 ARG cc_start: 0.7655 (mtt180) cc_final: 0.7013 (ptt90) REVERT: f 50 LEU cc_start: 0.8681 (mp) cc_final: 0.8351 (mp) REVERT: f 89 TYR cc_start: 0.8867 (m-10) cc_final: 0.8464 (m-80) REVERT: g 34 ARG cc_start: 0.7604 (ttp-110) cc_final: 0.7158 (ptm-80) REVERT: g 41 TYR cc_start: 0.7428 (m-80) cc_final: 0.7199 (m-80) REVERT: g 90 ARG cc_start: 0.7674 (mmt-90) cc_final: 0.7384 (ttp80) REVERT: h 75 GLU cc_start: 0.8792 (tp30) cc_final: 0.8311 (tp30) REVERT: i 44 ARG cc_start: 0.7157 (mtt-85) cc_final: 0.6857 (mtp85) REVERT: i 58 GLU cc_start: 0.8085 (tt0) cc_final: 0.7630 (tm-30) REVERT: i 104 ILE cc_start: 0.8998 (mm) cc_final: 0.8717 (mt) outliers start: 1 outliers final: 0 residues processed: 489 average time/residue: 0.1980 time to fit residues: 151.5124 Evaluate side-chains 369 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 177 optimal weight: 4.9990 chunk 6 optimal weight: 50.0000 chunk 137 optimal weight: 0.0030 chunk 3 optimal weight: 40.0000 chunk 88 optimal weight: 7.9990 chunk 126 optimal weight: 0.0010 chunk 35 optimal weight: 0.2980 chunk 186 optimal weight: 0.7980 chunk 269 optimal weight: 0.9980 chunk 176 optimal weight: 7.9990 chunk 156 optimal weight: 0.9980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 487 HIS P 160 HIS ** Y 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 207 HIS i 116 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.110740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.088445 restraints weight = 107818.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.088625 restraints weight = 160827.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.089681 restraints weight = 108141.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.089996 restraints weight = 71019.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.090310 restraints weight = 68325.635| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 30037 Z= 0.129 Angle : 0.609 14.874 41692 Z= 0.330 Chirality : 0.041 0.259 4949 Planarity : 0.005 0.164 4371 Dihedral : 23.993 170.538 6049 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.75 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.16), residues: 3051 helix: 1.40 (0.12), residues: 1933 sheet: -1.22 (0.35), residues: 238 loop : -2.05 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 119 TYR 0.045 0.002 TYR d 87 PHE 0.033 0.002 PHE I 546 TRP 0.011 0.001 TRP L 102 HIS 0.004 0.001 HIS f 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.13 (30037) covalent geometry : angle 0.60862 / 0.33 (41692) hydrogen bonds : bond 0.03870 / 4.10 ( 1857) hydrogen bonds : angle 3.76691 / 4.86 ( 5237) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 507 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 ARG cc_start: 0.7458 (tpt170) cc_final: 0.7249 (tpt90) REVERT: H 60 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7814 (tm-30) REVERT: I 536 ILE cc_start: 0.7451 (tt) cc_final: 0.6947 (tt) REVERT: I 612 LYS cc_start: 0.8525 (mttt) cc_final: 0.7980 (tptp) REVERT: K 108 ASN cc_start: 0.7942 (m-40) cc_final: 0.7467 (p0) REVERT: K 120 LYS cc_start: 0.8700 (mttt) cc_final: 0.8276 (tmtt) REVERT: L 121 MET cc_start: 0.8626 (mtp) cc_final: 0.8156 (mtp) REVERT: N 25 MET cc_start: 0.8151 (mmm) cc_final: 0.7886 (tpt) REVERT: N 140 TYR cc_start: 0.7400 (m-10) cc_final: 0.7188 (m-10) REVERT: N 217 LYS cc_start: 0.8526 (mmpt) cc_final: 0.8255 (tmtt) REVERT: N 397 ILE cc_start: 0.9459 (mm) cc_final: 0.9185 (mt) REVERT: O 201 MET cc_start: 0.8440 (mtp) cc_final: 0.8181 (ttp) REVERT: O 262 ASP cc_start: 0.7858 (p0) cc_final: 0.7237 (t0) REVERT: O 277 GLU cc_start: 0.8396 (tt0) cc_final: 0.7866 (tm-30) REVERT: O 321 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7745 (tm-30) REVERT: P 143 ASP cc_start: 0.7801 (p0) cc_final: 0.7301 (p0) REVERT: Q 239 SER cc_start: 0.9081 (m) cc_final: 0.8591 (t) REVERT: U 178 PHE cc_start: 0.7513 (m-80) cc_final: 0.7308 (m-10) REVERT: U 290 LEU cc_start: 0.7842 (pt) cc_final: 0.7043 (tp) REVERT: U 299 MET cc_start: 0.8918 (mmp) cc_final: 0.8702 (mmp) REVERT: U 308 LYS cc_start: 0.8824 (mttt) cc_final: 0.8380 (tttt) REVERT: U 312 ILE cc_start: 0.8286 (mt) cc_final: 0.7996 (tp) REVERT: Y 155 GLN cc_start: 0.8293 (mt0) cc_final: 0.7881 (mt0) REVERT: a 179 GLN cc_start: 0.7745 (mt0) cc_final: 0.7211 (mp10) REVERT: a 183 ILE cc_start: 0.7307 (mm) cc_final: 0.7103 (mm) REVERT: a 187 GLN cc_start: 0.7533 (pt0) cc_final: 0.7269 (pm20) REVERT: d 120 ARG cc_start: 0.7508 (mtt180) cc_final: 0.6979 (ptt90) REVERT: e 164 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7741 (tm-30) REVERT: f 50 LEU cc_start: 0.8748 (mp) cc_final: 0.8533 (tp) REVERT: f 69 ASP cc_start: 0.7668 (m-30) cc_final: 0.7462 (m-30) REVERT: f 89 TYR cc_start: 0.8869 (m-10) cc_final: 0.8461 (m-80) REVERT: g 41 TYR cc_start: 0.7476 (m-80) cc_final: 0.7233 (m-80) REVERT: g 90 ARG cc_start: 0.7654 (mmt-90) cc_final: 0.7370 (ttp80) REVERT: h 75 GLU cc_start: 0.8790 (tp30) cc_final: 0.8329 (tp30) REVERT: i 44 ARG cc_start: 0.7158 (mtt-85) cc_final: 0.6944 (mtt-85) REVERT: i 58 GLU cc_start: 0.8059 (tt0) cc_final: 0.7617 (tm-30) REVERT: i 59 TYR cc_start: 0.7521 (t80) cc_final: 0.7297 (t80) REVERT: i 104 ILE cc_start: 0.8860 (mm) cc_final: 0.8604 (mt) outliers start: 0 outliers final: 0 residues processed: 507 average time/residue: 0.1792 time to fit residues: 143.9409 Evaluate side-chains 378 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 256 optimal weight: 0.8980 chunk 4 optimal weight: 40.0000 chunk 277 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 225 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 280 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 317 optimal weight: 7.9990 chunk 301 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 88 ASN ** I 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 219 GLN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 200 HIS ** b 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 67 ASN i 75 ASN i 116 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.110075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.087803 restraints weight = 108722.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.088009 restraints weight = 183171.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.089281 restraints weight = 114929.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.089590 restraints weight = 74367.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.090073 restraints weight = 67184.011| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30037 Z= 0.140 Angle : 0.605 10.347 41692 Z= 0.330 Chirality : 0.041 0.251 4949 Planarity : 0.005 0.140 4371 Dihedral : 23.957 170.464 6049 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.79 % Favored : 95.15 % Rotamer: Outliers : 0.04 % Allowed : 2.22 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.16), residues: 3051 helix: 1.58 (0.12), residues: 1935 sheet: -1.08 (0.35), residues: 236 loop : -1.98 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG g 34 TYR 0.060 0.002 TYR d 87 PHE 0.028 0.001 PHE I 546 TRP 0.011 0.001 TRP L 102 HIS 0.006 0.001 HIS O 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (30037) covalent geometry : angle 0.60532 / 0.33 (41692) hydrogen bonds : bond 0.03880 / 4.08 ( 1857) hydrogen bonds : angle 3.72305 / 4.78 ( 5237) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 485 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 ARG cc_start: 0.7434 (tpt170) cc_final: 0.7218 (tpt90) REVERT: I 612 LYS cc_start: 0.8515 (mttt) cc_final: 0.7986 (tptp) REVERT: K 22 LYS cc_start: 0.8435 (mmtm) cc_final: 0.7839 (mmtm) REVERT: K 108 ASN cc_start: 0.7934 (m-40) cc_final: 0.7449 (p0) REVERT: K 120 LYS cc_start: 0.8659 (mttt) cc_final: 0.8280 (tmtt) REVERT: L 121 MET cc_start: 0.8720 (mtp) cc_final: 0.8328 (mtp) REVERT: L 238 GLN cc_start: 0.8379 (tp40) cc_final: 0.8168 (tp40) REVERT: N 25 MET cc_start: 0.8176 (mmm) cc_final: 0.7918 (tpt) REVERT: N 217 LYS cc_start: 0.8520 (mmpt) cc_final: 0.8290 (tmtt) REVERT: N 225 LEU cc_start: 0.9397 (tp) cc_final: 0.9136 (tp) REVERT: N 425 ASP cc_start: 0.7973 (m-30) cc_final: 0.7771 (m-30) REVERT: N 441 THR cc_start: 0.9005 (p) cc_final: 0.8766 (p) REVERT: O 201 MET cc_start: 0.8529 (mtp) cc_final: 0.8138 (ttp) REVERT: O 237 LYS cc_start: 0.9281 (mmtp) cc_final: 0.8860 (mmmm) REVERT: O 262 ASP cc_start: 0.7921 (p0) cc_final: 0.7212 (t0) REVERT: O 277 GLU cc_start: 0.8413 (tt0) cc_final: 0.7871 (tm-30) REVERT: P 143 ASP cc_start: 0.7285 (p0) cc_final: 0.7083 (p0) REVERT: Q 239 SER cc_start: 0.9085 (m) cc_final: 0.8620 (t) REVERT: U 178 PHE cc_start: 0.7485 (m-80) cc_final: 0.7281 (m-10) REVERT: U 290 LEU cc_start: 0.7787 (pt) cc_final: 0.7100 (tp) REVERT: U 308 LYS cc_start: 0.8806 (mttt) cc_final: 0.8352 (tttt) REVERT: U 312 ILE cc_start: 0.8264 (mt) cc_final: 0.7958 (tp) REVERT: Y 155 GLN cc_start: 0.8284 (mt0) cc_final: 0.7895 (mt0) REVERT: a 179 GLN cc_start: 0.7599 (mt0) cc_final: 0.7221 (mp10) REVERT: b 60 LYS cc_start: 0.8057 (pptt) cc_final: 0.7852 (pptt) REVERT: d 120 ARG cc_start: 0.7526 (mtt180) cc_final: 0.7001 (ptt90) REVERT: e 164 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7718 (tm-30) REVERT: f 89 TYR cc_start: 0.8848 (m-10) cc_final: 0.8449 (m-80) REVERT: g 41 TYR cc_start: 0.7447 (m-80) cc_final: 0.7197 (m-80) REVERT: h 75 GLU cc_start: 0.8760 (tp30) cc_final: 0.8317 (tp30) REVERT: i 58 GLU cc_start: 0.8030 (tt0) cc_final: 0.7604 (tm-30) REVERT: i 59 TYR cc_start: 0.7505 (t80) cc_final: 0.7262 (t80) REVERT: i 104 ILE cc_start: 0.8894 (mm) cc_final: 0.8624 (mt) outliers start: 1 outliers final: 0 residues processed: 486 average time/residue: 0.1766 time to fit residues: 135.9571 Evaluate side-chains 370 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 41 optimal weight: 9.9990 chunk 72 optimal weight: 40.0000 chunk 217 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 chunk 301 optimal weight: 10.0000 chunk 88 optimal weight: 0.0970 chunk 110 optimal weight: 0.7980 chunk 103 optimal weight: 0.0970 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 255 ASN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 76 HIS d 67 ASN h 67 ASN i 75 ASN i 116 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.110896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.088743 restraints weight = 109075.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.088557 restraints weight = 176824.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.089667 restraints weight = 122187.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.090147 restraints weight = 78895.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.090426 restraints weight = 73898.267| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 30037 Z= 0.127 Angle : 0.608 10.803 41692 Z= 0.330 Chirality : 0.041 0.243 4949 Planarity : 0.005 0.129 4371 Dihedral : 23.911 170.188 6049 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.59 % Favored : 95.38 % Rotamer: Outliers : 0.04 % Allowed : 2.13 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.16), residues: 3051 helix: 1.63 (0.12), residues: 1937 sheet: -1.01 (0.35), residues: 240 loop : -1.94 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG i 44 TYR 0.068 0.001 TYR d 87 PHE 0.036 0.001 PHE e 169 TRP 0.011 0.001 TRP L 102 HIS 0.021 0.001 HIS a 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 (30037) covalent geometry : angle 0.60844 / 0.33 (41692) hydrogen bonds : bond 0.03757 / 3.95 ( 1857) hydrogen bonds : angle 3.65864 / 4.68 ( 5237) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 499 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 ARG cc_start: 0.7424 (tpt170) cc_final: 0.7156 (tpt90) REVERT: I 612 LYS cc_start: 0.8524 (mttt) cc_final: 0.8000 (tptp) REVERT: K 22 LYS cc_start: 0.8424 (mmtm) cc_final: 0.7845 (mmtm) REVERT: K 108 ASN cc_start: 0.7937 (m-40) cc_final: 0.7504 (p0) REVERT: K 120 LYS cc_start: 0.8635 (mttt) cc_final: 0.8266 (tmtt) REVERT: L 74 ILE cc_start: 0.8996 (mm) cc_final: 0.8774 (mm) REVERT: L 121 MET cc_start: 0.8671 (mtp) cc_final: 0.8232 (mtp) REVERT: L 203 LEU cc_start: 0.9396 (mt) cc_final: 0.9151 (mt) REVERT: L 238 GLN cc_start: 0.8308 (tp40) cc_final: 0.8051 (tp40) REVERT: N 25 MET cc_start: 0.8182 (mmm) cc_final: 0.7930 (tpt) REVERT: N 107 LEU cc_start: 0.9482 (tp) cc_final: 0.9237 (tp) REVERT: N 217 LYS cc_start: 0.8507 (mmpt) cc_final: 0.8203 (tmtt) REVERT: N 326 LEU cc_start: 0.8975 (mp) cc_final: 0.8665 (tp) REVERT: N 408 ASP cc_start: 0.8408 (t0) cc_final: 0.8194 (t70) REVERT: O 201 MET cc_start: 0.8517 (mtp) cc_final: 0.8162 (ttp) REVERT: O 237 LYS cc_start: 0.9243 (mmtp) cc_final: 0.8830 (mmmm) REVERT: O 262 ASP cc_start: 0.8014 (p0) cc_final: 0.7289 (t0) REVERT: O 277 GLU cc_start: 0.8442 (tt0) cc_final: 0.7934 (tm-30) REVERT: P 143 ASP cc_start: 0.7349 (p0) cc_final: 0.7135 (p0) REVERT: Q 239 SER cc_start: 0.9062 (m) cc_final: 0.8626 (t) REVERT: U 201 GLU cc_start: 0.6792 (pt0) cc_final: 0.6560 (pt0) REVERT: U 290 LEU cc_start: 0.7858 (pt) cc_final: 0.7023 (tp) REVERT: U 299 MET cc_start: 0.9061 (mmp) cc_final: 0.8807 (mmp) REVERT: U 308 LYS cc_start: 0.8849 (mttt) cc_final: 0.8385 (tptt) REVERT: U 312 ILE cc_start: 0.8301 (mt) cc_final: 0.8005 (tp) REVERT: Y 155 GLN cc_start: 0.8323 (mt0) cc_final: 0.7978 (mt0) REVERT: a 179 GLN cc_start: 0.7504 (mt0) cc_final: 0.7026 (mp10) REVERT: d 67 ASN cc_start: 0.8657 (OUTLIER) cc_final: 0.8457 (t0) REVERT: d 120 ARG cc_start: 0.7517 (mtt180) cc_final: 0.6994 (ptt90) REVERT: e 164 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7714 (tm-30) REVERT: e 222 ARG cc_start: 0.7861 (mtp85) cc_final: 0.7054 (mtp-110) REVERT: f 50 LEU cc_start: 0.8621 (tp) cc_final: 0.7933 (mp) REVERT: f 89 TYR cc_start: 0.8863 (m-10) cc_final: 0.8445 (m-80) REVERT: g 41 TYR cc_start: 0.7406 (m-80) cc_final: 0.7085 (m-80) REVERT: h 63 MET cc_start: 0.7571 (mmm) cc_final: 0.7321 (mmm) REVERT: h 75 GLU cc_start: 0.8811 (tp30) cc_final: 0.8363 (tp30) REVERT: i 58 GLU cc_start: 0.8083 (tt0) cc_final: 0.7629 (tm-30) REVERT: i 59 TYR cc_start: 0.7442 (t80) cc_final: 0.7203 (t80) REVERT: i 104 ILE cc_start: 0.8852 (mm) cc_final: 0.8421 (mt) outliers start: 1 outliers final: 0 residues processed: 500 average time/residue: 0.2030 time to fit residues: 161.0333 Evaluate side-chains 375 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 374 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 225 optimal weight: 9.9990 chunk 240 optimal weight: 0.8980 chunk 147 optimal weight: 0.6980 chunk 252 optimal weight: 3.9990 chunk 191 optimal weight: 9.9990 chunk 73 optimal weight: 30.0000 chunk 198 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 277 optimal weight: 9.9990 chunk 189 optimal weight: 10.0000 chunk 158 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 47 HIS I 398 GLN ** I 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 213 HIS ** P 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 217 ASN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 76 HIS i 75 ASN i 114 HIS i 116 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.109735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.087454 restraints weight = 108797.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.088052 restraints weight = 201171.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.089313 restraints weight = 115946.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.089534 restraints weight = 77117.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.089982 restraints weight = 68751.597| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30037 Z= 0.163 Angle : 0.632 10.446 41692 Z= 0.342 Chirality : 0.042 0.253 4949 Planarity : 0.005 0.094 4371 Dihedral : 23.899 170.365 6049 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.04 % Allowed : 1.35 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.16), residues: 3051 helix: 1.73 (0.12), residues: 1934 sheet: -1.03 (0.36), residues: 241 loop : -1.92 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG Y 100 TYR 0.077 0.002 TYR d 87 PHE 0.019 0.002 PHE b 101 TRP 0.010 0.001 TRP I 472 HIS 0.014 0.001 HIS a 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (30037) covalent geometry : angle 0.63206 / 0.34 (41692) hydrogen bonds : bond 0.03954 / 4.12 ( 1857) hydrogen bonds : angle 3.71850 / 4.75 ( 5237) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 464 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 ARG cc_start: 0.7317 (tpt170) cc_final: 0.7062 (tpt90) REVERT: I 612 LYS cc_start: 0.8534 (mttt) cc_final: 0.8003 (tptp) REVERT: K 22 LYS cc_start: 0.8417 (mmtm) cc_final: 0.7846 (mmtm) REVERT: K 108 ASN cc_start: 0.7867 (m-40) cc_final: 0.7456 (p0) REVERT: K 120 LYS cc_start: 0.8651 (mttt) cc_final: 0.8296 (tmtt) REVERT: L 121 MET cc_start: 0.8731 (mtp) cc_final: 0.8342 (mtp) REVERT: N 25 MET cc_start: 0.8193 (mmm) cc_final: 0.7935 (tpt) REVERT: N 107 LEU cc_start: 0.9557 (tp) cc_final: 0.9318 (tp) REVERT: N 217 LYS cc_start: 0.8469 (mmpt) cc_final: 0.8223 (tmtt) REVERT: N 425 ASP cc_start: 0.8064 (m-30) cc_final: 0.7848 (m-30) REVERT: O 201 MET cc_start: 0.8623 (mtp) cc_final: 0.8247 (ttp) REVERT: O 237 LYS cc_start: 0.9261 (mmtp) cc_final: 0.8821 (mmmm) REVERT: O 262 ASP cc_start: 0.7967 (p0) cc_final: 0.7312 (t0) REVERT: O 277 GLU cc_start: 0.8401 (tt0) cc_final: 0.7898 (tm-30) REVERT: Q 239 SER cc_start: 0.9099 (m) cc_final: 0.8611 (t) REVERT: U 290 LEU cc_start: 0.7712 (pt) cc_final: 0.6985 (tp) REVERT: U 308 LYS cc_start: 0.8833 (mttt) cc_final: 0.8383 (tttt) REVERT: U 312 ILE cc_start: 0.8239 (mt) cc_final: 0.7928 (tp) REVERT: Y 139 VAL cc_start: 0.8363 (p) cc_final: 0.7910 (p) REVERT: Y 155 GLN cc_start: 0.8273 (mt0) cc_final: 0.7888 (mt0) REVERT: a 179 GLN cc_start: 0.7520 (mt0) cc_final: 0.7065 (mp10) REVERT: d 120 ARG cc_start: 0.7657 (mtt180) cc_final: 0.7005 (ptt90) REVERT: e 164 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7630 (tm-30) REVERT: f 69 ASP cc_start: 0.7857 (m-30) cc_final: 0.7548 (m-30) REVERT: f 92 LYS cc_start: 0.9551 (tmtt) cc_final: 0.9323 (tmtt) REVERT: g 41 TYR cc_start: 0.7436 (m-80) cc_final: 0.7159 (m-80) REVERT: h 75 GLU cc_start: 0.8748 (tp30) cc_final: 0.8289 (tp30) REVERT: h 87 TYR cc_start: 0.8843 (m-10) cc_final: 0.8530 (m-10) REVERT: i 58 GLU cc_start: 0.7987 (tt0) cc_final: 0.7566 (tm-30) REVERT: i 104 ILE cc_start: 0.8907 (mm) cc_final: 0.8493 (mt) REVERT: i 114 HIS cc_start: 0.6482 (t-90) cc_final: 0.5996 (t70) outliers start: 1 outliers final: 1 residues processed: 465 average time/residue: 0.1990 time to fit residues: 147.7009 Evaluate side-chains 368 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 367 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 74 optimal weight: 4.9990 chunk 307 optimal weight: 9.9990 chunk 301 optimal weight: 0.0870 chunk 250 optimal weight: 8.9990 chunk 228 optimal weight: 20.0000 chunk 256 optimal weight: 3.9990 chunk 272 optimal weight: 20.0000 chunk 287 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 overall best weight: 2.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 HIS ** P 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 217 ASN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 67 ASN ** e 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 ASN i 75 ASN i 116 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.108300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.086137 restraints weight = 109729.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.087593 restraints weight = 209115.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.088511 restraints weight = 101117.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.088501 restraints weight = 82569.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.089053 restraints weight = 70067.082| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 30037 Z= 0.219 Angle : 0.687 12.215 41692 Z= 0.368 Chirality : 0.043 0.265 4949 Planarity : 0.005 0.082 4371 Dihedral : 23.979 170.622 6049 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.13 % Favored : 93.84 % Rotamer: Outliers : 0.04 % Allowed : 0.74 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.16), residues: 3051 helix: 1.64 (0.12), residues: 1949 sheet: -1.07 (0.36), residues: 238 loop : -2.00 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG a 210 TYR 0.063 0.002 TYR d 87 PHE 0.022 0.002 PHE U 295 TRP 0.015 0.002 TRP I 472 HIS 0.015 0.001 HIS a 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.22 (30037) covalent geometry : angle 0.68653 / 0.37 (41692) hydrogen bonds : bond 0.04358 / 4.53 ( 1857) hydrogen bonds : angle 3.88784 / 5.01 ( 5237) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 455 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 ARG cc_start: 0.7397 (tpt170) cc_final: 0.7107 (tpt90) REVERT: I 440 MET cc_start: 0.8212 (mmm) cc_final: 0.7987 (mmm) REVERT: I 468 MET cc_start: 0.8405 (ttp) cc_final: 0.8186 (tmm) REVERT: I 612 LYS cc_start: 0.8552 (mttt) cc_final: 0.8021 (tptp) REVERT: K 22 LYS cc_start: 0.8446 (mmtm) cc_final: 0.7864 (mmtm) REVERT: K 108 ASN cc_start: 0.7962 (m-40) cc_final: 0.7498 (p0) REVERT: K 120 LYS cc_start: 0.8655 (mttt) cc_final: 0.8310 (tmtt) REVERT: L 121 MET cc_start: 0.8734 (mtp) cc_final: 0.8308 (mtp) REVERT: L 198 MET cc_start: 0.8558 (mtp) cc_final: 0.8262 (mtp) REVERT: N 25 MET cc_start: 0.8261 (mmm) cc_final: 0.7889 (tpt) REVERT: N 124 GLN cc_start: 0.8261 (mp10) cc_final: 0.8043 (mp10) REVERT: N 443 MET cc_start: 0.7840 (tpp) cc_final: 0.7515 (tpp) REVERT: O 237 LYS cc_start: 0.9231 (mmtp) cc_final: 0.8810 (mmmm) REVERT: O 262 ASP cc_start: 0.8073 (p0) cc_final: 0.7354 (t0) REVERT: O 277 GLU cc_start: 0.8528 (tt0) cc_final: 0.7917 (tm-30) REVERT: P 347 GLU cc_start: 0.8525 (pp20) cc_final: 0.7949 (pp20) REVERT: Q 239 SER cc_start: 0.9113 (m) cc_final: 0.8635 (t) REVERT: U 299 MET cc_start: 0.8830 (mmp) cc_final: 0.8484 (mmp) REVERT: U 308 LYS cc_start: 0.8854 (mttt) cc_final: 0.8398 (tttt) REVERT: U 312 ILE cc_start: 0.8262 (mt) cc_final: 0.7993 (tp) REVERT: Y 96 GLU cc_start: 0.7581 (tp30) cc_final: 0.7337 (tp30) REVERT: Y 155 GLN cc_start: 0.8275 (mt0) cc_final: 0.7935 (mt0) REVERT: a 179 GLN cc_start: 0.7541 (mt0) cc_final: 0.7212 (mp10) REVERT: d 120 ARG cc_start: 0.7794 (mtt180) cc_final: 0.7148 (ptt90) REVERT: e 146 GLN cc_start: 0.6299 (mp10) cc_final: 0.5861 (mp10) REVERT: e 164 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7637 (tm-30) REVERT: e 222 ARG cc_start: 0.7797 (mtp85) cc_final: 0.6980 (mtp85) REVERT: f 69 ASP cc_start: 0.7753 (m-30) cc_final: 0.6981 (m-30) REVERT: f 92 LYS cc_start: 0.9532 (tmtt) cc_final: 0.9290 (tmtt) REVERT: h 75 GLU cc_start: 0.8801 (tp30) cc_final: 0.8355 (tp30) REVERT: h 87 TYR cc_start: 0.8937 (m-10) cc_final: 0.8718 (m-80) REVERT: i 58 GLU cc_start: 0.8022 (tt0) cc_final: 0.7484 (tm-30) REVERT: i 104 ILE cc_start: 0.8840 (mm) cc_final: 0.8391 (mt) REVERT: i 114 HIS cc_start: 0.6761 (t-90) cc_final: 0.6120 (t70) outliers start: 1 outliers final: 1 residues processed: 456 average time/residue: 0.1994 time to fit residues: 145.5732 Evaluate side-chains 358 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 16 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 280 optimal weight: 0.8980 chunk 261 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 chunk 260 optimal weight: 20.0000 chunk 156 optimal weight: 0.9990 chunk 283 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 47 HIS I 467 GLN ** I 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 213 HIS ** P 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 76 HIS d 113 HIS ** e 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 75 ASN i 116 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.109204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.086863 restraints weight = 108431.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.087180 restraints weight = 194989.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.088419 restraints weight = 116661.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.088698 restraints weight = 76420.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.089074 restraints weight = 70485.026| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30037 Z= 0.150 Angle : 0.647 11.651 41692 Z= 0.348 Chirality : 0.042 0.258 4949 Planarity : 0.004 0.078 4371 Dihedral : 23.969 169.845 6049 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.04 % Allowed : 0.62 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.16), residues: 3051 helix: 1.74 (0.12), residues: 1939 sheet: -1.00 (0.37), residues: 229 loop : -1.95 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG b 79 TYR 0.033 0.002 TYR d 87 PHE 0.029 0.002 PHE I 463 TRP 0.013 0.001 TRP L 102 HIS 0.013 0.001 HIS a 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (30037) covalent geometry : angle 0.64741 / 0.35 (41692) hydrogen bonds : bond 0.03995 / 4.21 ( 1857) hydrogen bonds : angle 3.79483 / 4.86 ( 5237) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 450 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 ARG cc_start: 0.7362 (tpt170) cc_final: 0.7099 (tpt90) REVERT: I 612 LYS cc_start: 0.8586 (mttt) cc_final: 0.8029 (tptp) REVERT: I 702 MET cc_start: 0.7170 (ttm) cc_final: 0.6930 (ttp) REVERT: K 22 LYS cc_start: 0.8464 (mmtm) cc_final: 0.7925 (mmtm) REVERT: K 108 ASN cc_start: 0.7919 (m-40) cc_final: 0.7445 (p0) REVERT: K 120 LYS cc_start: 0.8643 (mttt) cc_final: 0.8291 (tmtt) REVERT: L 121 MET cc_start: 0.8765 (mtp) cc_final: 0.8383 (mtp) REVERT: N 25 MET cc_start: 0.8233 (mmm) cc_final: 0.7984 (tpt) REVERT: N 124 GLN cc_start: 0.8171 (mp10) cc_final: 0.7932 (mp10) REVERT: N 201 TYR cc_start: 0.8361 (m-80) cc_final: 0.8129 (m-80) REVERT: N 217 LYS cc_start: 0.8471 (mmpt) cc_final: 0.8235 (tmtt) REVERT: N 326 LEU cc_start: 0.9118 (mp) cc_final: 0.8670 (tp) REVERT: O 201 MET cc_start: 0.8500 (mtp) cc_final: 0.8195 (ttp) REVERT: O 237 LYS cc_start: 0.9273 (mmtp) cc_final: 0.8838 (mmmm) REVERT: O 262 ASP cc_start: 0.7984 (p0) cc_final: 0.7414 (t0) REVERT: O 277 GLU cc_start: 0.8468 (tt0) cc_final: 0.7875 (tm-30) REVERT: P 347 GLU cc_start: 0.8522 (pp20) cc_final: 0.7968 (pp20) REVERT: Q 239 SER cc_start: 0.9112 (m) cc_final: 0.8602 (t) REVERT: Q 374 MET cc_start: 0.7593 (mtp) cc_final: 0.7228 (mtp) REVERT: U 290 LEU cc_start: 0.7748 (pt) cc_final: 0.7034 (tp) REVERT: U 299 MET cc_start: 0.8824 (mmp) cc_final: 0.8487 (mmp) REVERT: U 308 LYS cc_start: 0.8821 (mttt) cc_final: 0.8366 (tttt) REVERT: U 312 ILE cc_start: 0.8293 (mt) cc_final: 0.8032 (tp) REVERT: Y 96 GLU cc_start: 0.7420 (tp30) cc_final: 0.7146 (tp30) REVERT: Y 155 GLN cc_start: 0.8247 (mt0) cc_final: 0.7853 (mt0) REVERT: a 179 GLN cc_start: 0.7665 (mt0) cc_final: 0.7244 (mp10) REVERT: d 120 ARG cc_start: 0.7718 (mtt180) cc_final: 0.7109 (ptt90) REVERT: e 144 LYS cc_start: 0.9122 (tppt) cc_final: 0.8840 (tppt) REVERT: e 164 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7679 (tm-30) REVERT: e 222 ARG cc_start: 0.7698 (mtp85) cc_final: 0.6868 (mtp85) REVERT: f 69 ASP cc_start: 0.7604 (m-30) cc_final: 0.7214 (m-30) REVERT: f 92 LYS cc_start: 0.9519 (tmtt) cc_final: 0.9283 (tmtt) REVERT: g 27 PHE cc_start: 0.6420 (m-80) cc_final: 0.6120 (m-10) REVERT: g 41 TYR cc_start: 0.7377 (m-80) cc_final: 0.7141 (m-80) REVERT: h 75 GLU cc_start: 0.8811 (tp30) cc_final: 0.8370 (tp30) REVERT: i 58 GLU cc_start: 0.8110 (tt0) cc_final: 0.7563 (tm-30) REVERT: i 104 ILE cc_start: 0.8826 (mm) cc_final: 0.8391 (mt) REVERT: i 114 HIS cc_start: 0.6760 (t-90) cc_final: 0.6206 (t70) outliers start: 1 outliers final: 1 residues processed: 451 average time/residue: 0.1944 time to fit residues: 140.8426 Evaluate side-chains 364 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 363 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 308 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 254 optimal weight: 6.9990 chunk 4 optimal weight: 40.0000 chunk 8 optimal weight: 30.0000 chunk 263 optimal weight: 10.0000 chunk 92 optimal weight: 0.0670 chunk 22 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 76 HIS d 67 ASN d 113 HIS ** e 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 75 ASN i 116 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.109337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.087131 restraints weight = 108879.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.087132 restraints weight = 183543.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.088274 restraints weight = 115444.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.088685 restraints weight = 76087.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.089028 restraints weight = 69925.716| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30037 Z= 0.150 Angle : 0.649 16.459 41692 Z= 0.347 Chirality : 0.042 0.257 4949 Planarity : 0.004 0.093 4371 Dihedral : 23.941 169.461 6049 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.04 % Allowed : 0.41 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.16), residues: 3051 helix: 1.75 (0.12), residues: 1941 sheet: -0.99 (0.37), residues: 229 loop : -1.92 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG g 38 TYR 0.035 0.002 TYR H 23 PHE 0.021 0.002 PHE I 463 TRP 0.011 0.001 TRP L 102 HIS 0.012 0.001 HIS a 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (30037) covalent geometry : angle 0.64947 / 0.35 (41692) hydrogen bonds : bond 0.03982 / 4.21 ( 1857) hydrogen bonds : angle 3.78564 / 4.86 ( 5237) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4841.58 seconds wall clock time: 84 minutes 40.28 seconds (5080.28 seconds total)